The security of Nato's main supply line into Afghanistan came under threat on Saturday as Pakistani parliamentarians voted to review all aspects of their relationship with the US amid worsening political fallout from the raid that killed Osama bin Laden.

The unanimous motion was passed in the early hours of Saturday morning at the conclusion of an extraordinary 10-hour parliamentary session when the military's top brass offered apologies and admissions of failure, and the country's spy chief offered to resign.

Condemning the 2 May raid on bin Laden's house in Abbottabad, 35 miles northeast of Islamabad, as a "violation of Pakistan's sovereignty", parliament voted unanimously to review the country's terms of engagement with Washington.

In feisty speeches lawmakers warned against further "unilateral action", including CIA drone strikes, and urged the government to consider cutting the Nato supply line that runs from Karachi to Afghanistan through the Khyber Pass and Balochistan.

Suspicious of Pakistan's failure to capture bin Laden but recognising the importance of the supply line and pursuing other al-Qaida fugitives, the Obama administration is dispatching Senator John Kerry – the "good cop" of US diplomacy with Pakistan – to Islamabad on Sunday.

"We're not trying to find a way to break the relationship apart, we're trying to find a way to build it," he told reporters in Kabul on Saturday.

Kerry arrives in Pakistan at a time of unprecedented criticism of the powerful military. On Friday night top generals were submitted to harsh questioning from parliamentarians during a marathon session that stretched late into the night.

The inter-services intelligence (ISI) chief General Shuja Pasha, one of the most powerful figures in the country, admitted to an "intelligence failure" on Bin Laden, insisting that the ISI had been kept in the "complete dark" by the US over the raid, and tendered his resignation to prime minister Yousaf Raza Gilani. It was not accepted – a sign that the government, led by Asif Ali Zardari, has decided to support the weakened military.

The fragile civilian government is gambling that its pro-army stance will guarantee it a full term in office. "It was politically a very astute move," said Talat Masood, a retired general and political analyst.

Another striking revelation came from the deputy air force chief, who admitted that CIA drones take off from Shamsi airbase in Balochistan province. But he insisted that the drones were unarmed – those carrying missiles came from Afghanistan, he said – and that Shamsi was actually under the authority of the United Arab Emirates, which built the remote airstrip in the 1990s for rich sheikhs on bird-hunting expeditions.

Despite having been technically held in camera, details of the parliamentary session leaked out to the media. One MP told the news website Dawn that the air force chief claimed to have ordered his jet fighters to shoot down US helicopters with Bin Laden's body on board when they were leaving Pakistan, but they were too slow.

Although generally apologetic, in some instances the generals struck back at their critics. When an MP from a religious party attacked Pasha, the spy chief told the mullah that was in no position to talk because he had received funds from Libya and Saudi Arabia.

The parliamentary motion appeared intended to deflect attention from uncomfortable questions about Bin Laden's Pakistan sanctuary onto complaints about US breaches of sovereignty. But the opposition leader, Nawaz Sharif, who was ousted from power in a 1999 military coup, said he was determined to seek greater accountability of army power. "The elected government should formulate foreign policy. A parallel policy or parallel government should not be allowed to work," he told a news conference yesterday.

Deteriorating relations with the US are further complicated by a bitter row between spies on both sides. The fact that the CIA could run such a massive operation to capture Bin Laden had deeply embarrassed the ISI, said Vali Nasr, a former Obama administration advisor. "It's not just a diplomatic embarrassment, it's a counter-espionage failure," he said. "Suddenly the ISI is scared of what the CIA is capable of doing."

In a further sign of cooling relations General Khalid Wynne, chairman of Pakistan's joint chiefs of staff committee, has cancelled a five-day visit to the United States due to start on 22 May.

The US has begun to look to central Asian countries to reduce its reliance on Pakistan for military supplies to Afghanistan. The cricketer-turned-politician Imran Khan has already threatened to have his supporters block military trucks passing through Peshawar.

But outside parliament, the gap between political rhetoric and ground realities is as stark as ever in Pakistan. On Friday a CIA drone fired missiles that killed five people in the tribal belt, the fourth such attack since 2 May.

Yesterday the death toll from Friday's Taliban suicide attack on a paramilitary training centre climbed to 89; a Taliban spokesman said the vicious bombing was to avenge the al-Qaida leader's death and warned of more to come.